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How to find the transcription factor that binds to a known sequence?


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#1 kikihan

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Posted 11 March 2009 - 07:33 AM

Hi I am a beginner of genomics. I have got some predicted enhancers (their beginning and ending sites in the genome are known) in the genome, and now I wanna predict which transcription factors would bind to these "predicted enhancers". So is there any online softwares that have such function? Thanks for your help!

#2 Dr Teeth

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Posted 11 March 2009 - 09:42 AM

Try:
TF Seach at http://www.cbrc.jp/r...b/TFSEARCH.html
Cister (Cis element cluster finder) at http://zlab.bu.edu/~...th/cister.shtml
WWW promoter scan at http://www-bimas.cit...molbio/proscan/

These will work for general transcription factors like HNFs, Sp1, AP-1, NFkB, etc.
None that I am aware of predict binding of nuclear receptors etc.

Science is simply common sense at its best that is rigidly accurate in observation and merciless to fallacy in logic.
Thomas Henry Huxley

#3 kikihan

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Posted 11 March 2009 - 10:26 AM

Thanks~ but These tools are for predicting TF binding sites actually, yet I was asking about the other way, that is from known enhancers (databases) to the TFs that bind to them.

Try:
TF Seach at http://www.cbrc.jp/r...b/TFSEARCH.html
Cister (Cis element cluster finder) at http://zlab.bu.edu/~...th/cister.shtml
WWW promoter scan at http://www-bimas.cit...molbio/proscan/

These will work for general transcription factors like HNFs, Sp1, AP-1, NFkB, etc.
None that I am aware of predict binding of nuclear receptors etc.






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